Bernal Jiménez Gutiérrez

Bernal Jiménez Gutiérrez, Nikolas McNeal, Clay Washington et al. · microsoft-research

The strong few-shot in-context learning capability of large pre-trained language models (PLMs) such as GPT-3 is highly appealing for application domains such as biomedicine, which feature high and diverse demands of language technologies but also high data annotation costs. In this paper, we present the first systematic and comprehensive study to compare the few-shot performance of GPT-3 in-context learning with fine-tuning smaller (i.e., BERT-sized) PLMs on two highly representative biomedical information extraction tasks, named entity recognition and relation extraction. We follow the true few-shot setting to avoid overestimating models' few-shot performance by model selection over a large validation set. We also optimize GPT-3's performance with known techniques such as contextual calibration and dynamic in-context example retrieval. However, our results show that GPT-3 still significantly underperforms compared to simply fine-tuning a smaller PLM. In addition, GPT-3 in-context learning also yields smaller gains in accuracy when more training data becomes available. Our in-depth analyses further reveal issues of the in-context learning setting that may be detrimental to information extraction tasks in general. Given the high cost of experimenting with GPT-3, we hope our study provides guidance for biomedical researchers and practitioners towards more promising directions such as fine-tuning small PLMs.

Bernal Jiménez Gutiérrez, Huan Sun, Yu Su · microsoft-research

As opposed to general English, many concepts in biomedical terminology have been designed in recent history by biomedical professionals with the goal of being precise and concise. This is often achieved by concatenating meaningful biomedical morphemes to create new semantic units. Nevertheless, most modern biomedical language models (LMs) are pre-trained using standard domain-specific tokenizers derived from large scale biomedical corpus statistics without explicitly leveraging the agglutinating nature of biomedical language. In this work, we first find that standard open-domain and biomedical tokenizers are largely unable to segment biomedical terms into meaningful components. Therefore, we hypothesize that using a tokenizer which segments biomedical terminology more accurately would enable biomedical LMs to improve their performance on downstream biomedical NLP tasks, especially ones which involve biomedical terms directly such as named entity recognition (NER) and entity linking. Surprisingly, we find that pre-training a biomedical LM using a more accurate biomedical tokenizer does not improve the entity representation quality of a language model as measured by several intrinsic and extrinsic measures such as masked language modeling prediction (MLM) accuracy as well as NER and entity linking performance. These quantitative findings, along with a case study which explores entity representation quality more directly, suggest that the biomedical pre-training process is quite robust to instances of sub-optimal tokenization.

Yiheng Shu, Bernal Jiménez Gutiérrez, Saisri Padmaja Jonnalagedda et al.

Language agents spend substantial inference time solving individual tasks, yet the experience acquired in one episode is often underutilized in future episodes. Continual learning expects an agent to accumulate reusable experience across a stream of tasks, improve over time, and avoid interference from irrelevant experiences. Unfortunately, existing benchmarks struggle to evaluate continual learning in language agents rigorously. Most efforts focus on retrieval and reasoning over long-context conversations or documents, while recent lifelong-adaptation benchmarks often rely on naive task streams with limited analysis of cross-task relationships, making it difficult to understand what an agent learns and reuses over time. This paper presents an evaluation framework AgentCL for continual learning in agents, centered on controlled task streams and metrics for transfer gains. AGENTCL constructs compositional streams where earlier sub-solutions, evidence, or workflows are intentionally reusable in later tasks, and contrasts them with naive streams where such reusability is not guaranteed. We use the benchmark to evaluate non-parametric memory designs for continual learning. To diagnose how memory design choices affect continual learning, we develop MemProbe, a probing method that stores interactions, insights, and skills, while filtering unreliable experiences during consolidation. Empirical analysis across coding, deep research, and language understanding/reasoning tasks shows that naive streams offer limited ability to distinguish memory designs, whereas controlled streams more clearly distinguish their plasticity. Meanwhile, naive and held-out settings often yield limited gains and can expose memory-induced degradation. These results highlight the need for stronger memory designs that balance plasticity and stable reuse.

Bernal Jiménez Gutiérrez, Yiheng Shu, Yu Gu et al. · microsoft-research

In order to thrive in hostile and ever-changing natural environments, mammalian brains evolved to store large amounts of knowledge about the world and continually integrate new information while avoiding catastrophic forgetting. Despite the impressive accomplishments, large language models (LLMs), even with retrieval-augmented generation (RAG), still struggle to efficiently and effectively integrate a large amount of new experiences after pre-training. In this work, we introduce HippoRAG, a novel retrieval framework inspired by the hippocampal indexing theory of human long-term memory to enable deeper and more efficient knowledge integration over new experiences. HippoRAG synergistically orchestrates LLMs, knowledge graphs, and the Personalized PageRank algorithm to mimic the different roles of neocortex and hippocampus in human memory. We compare HippoRAG with existing RAG methods on multi-hop question answering and show that our method outperforms the state-of-the-art methods remarkably, by up to 20%. Single-step retrieval with HippoRAG achieves comparable or better performance than iterative retrieval like IRCoT while being 10-30 times cheaper and 6-13 times faster, and integrating HippoRAG into IRCoT brings further substantial gains. Finally, we show that our method can tackle new types of scenarios that are out of reach of existing methods. Code and data are available at https://github.com/OSU-NLP-Group/HippoRAG.

Bernal Jiménez Gutiérrez, Yiheng Shu, Weijian Qi et al. · microsoft-research

Our ability to continuously acquire, organize, and leverage knowledge is a key feature of human intelligence that AI systems must approximate to unlock their full potential. Given the challenges in continual learning with large language models (LLMs), retrieval-augmented generation (RAG) has become the dominant way to introduce new information. However, its reliance on vector retrieval hinders its ability to mimic the dynamic and interconnected nature of human long-term memory. Recent RAG approaches augment vector embeddings with various structures like knowledge graphs to address some of these gaps, namely sense-making and associativity. However, their performance on more basic factual memory tasks drops considerably below standard RAG. We address this unintended deterioration and propose HippoRAG 2, a framework that outperforms standard RAG comprehensively on factual, sense-making, and associative memory tasks. HippoRAG 2 builds upon the Personalized PageRank algorithm used in HippoRAG and enhances it with deeper passage integration and more effective online use of an LLM. This combination pushes this RAG system closer to the effectiveness of human long-term memory, achieving a 7% improvement in associative memory tasks over the state-of-the-art embedding model while also exhibiting superior factual knowledge and sense-making memory capabilities. This work paves the way for non-parametric continual learning for LLMs. Code and data are available at https://github.com/OSU-NLP-Group/HippoRAG.

Yiheng Shu, Saisri Padmaja Jonnalagedda, Xiang Gao et al.

Humans excel at remembering concrete experiences along spatiotemporal contexts and performing reasoning across those events, i.e., the capacity for episodic memory. In contrast, memory in language agents remains mainly semantic, and current agents are not yet capable of effectively recollecting and reasoning over interaction histories. We identify and formalize the core challenges of episodic recollection and reasoning from this gap, and observe that existing work often overlooks episodicity, lacks explicit event modeling, or overemphasizes simple retrieval rather than complex reasoning. We present REMem, a two-phase framework for constructing and reasoning with episodic memory: 1) Offline indexing, where REMem converts experiences into a hybrid memory graph that flexibly links time-aware gists and facts. 2) Online inference, where REMem employs an agentic retriever with carefully curated tools for iterative retrieval over the memory graph. Comprehensive evaluation across four episodic memory benchmarks shows that REMem substantially outperforms state-of-the-art memory systems such as Mem0 and HippoRAG 2, showing 3.4% and 13.4% absolute improvements on episodic recollection and reasoning tasks, respectively. Moreover, REMem also demonstrates more robust refusal behavior for unanswerable questions.

Boyu Gou, Zanming Huang, Yuting Ning et al. · microsoft-research

Agentic search such as Deep Research systems-where agents autonomously browse the web, synthesize information, and return comprehensive citation-backed answers-represents a major shift in how users interact with web-scale information. While promising greater efficiency and cognitive offloading, the growing complexity and open-endedness of agentic search have outpaced existing evaluation benchmarks and methodologies, which largely assume short search horizons and static answers. In this paper, we introduce Mind2Web 2, a benchmark of 130 realistic, high-quality, and long-horizon tasks that require real-time web browsing and extensive information synthesis, constructed with over 1000 hours of human labor. To address the challenge of evaluating time-varying and complex answers, we propose a novel Agent-as-a-Judge framework. Our method constructs task-specific judge agents based on a tree-structured rubric design to automatically assess both answer correctness and source attribution. We conduct a comprehensive evaluation of ten frontier agentic search systems and human performance, along with a detailed error analysis to draw insights for future development. The best-performing system, OpenAI Deep Research, can already achieve 50-70% of human performance while spending half the time, highlighting its great potential. Altogether, Mind2Web 2 provides a rigorous foundation for developing and benchmarking the next generation of agentic search systems.

Kai Zhang, Bernal Jiménez Gutiérrez, Yu Su

Recent work has shown that fine-tuning large language models (LLMs) on large-scale instruction-following datasets substantially improves their performance on a wide range of NLP tasks, especially in the zero-shot setting. However, even advanced instruction-tuned LLMs still fail to outperform small LMs on relation extraction (RE), a fundamental information extraction task. We hypothesize that instruction-tuning has been unable to elicit strong RE capabilities in LLMs due to RE's low incidence in instruction-tuning datasets, making up less than 1% of all tasks (Wang et al., 2022). To address this limitation, we propose QA4RE, a framework that aligns RE with question answering (QA), a predominant task in instruction-tuning datasets. Comprehensive zero-shot RE experiments over four datasets with two series of instruction-tuned LLMs (six LLMs in total) demonstrate that our QA4RE framework consistently improves LLM performance, strongly verifying our hypothesis and enabling LLMs to outperform strong zero-shot baselines by a large margin. Additionally, we provide thorough experiments and discussions to show the robustness, few-shot effectiveness, and strong transferability of our QA4RE framework. This work illustrates a promising way of adapting LLMs to challenging and underrepresented tasks by aligning these tasks with more common instruction-tuning tasks like QA.

Bernal Jiménez Gutiérrez, Juncheng Zeng, Dongdong Zhang et al.

The global pandemic has made it more important than ever to quickly and accurately retrieve relevant scientific literature for effective consumption by researchers in a wide range of fields. We provide an analysis of several multi-label document classification models on the LitCovid dataset, a growing collection of 23,000 research papers regarding the novel 2019 coronavirus. We find that pre-trained language models fine-tuned on this dataset outperform all other baselines and that BioBERT surpasses the others by a small margin with micro-F1 and accuracy scores of around 86% and 75% respectively on the test set. We evaluate the data efficiency and generalizability of these models as essential features of any system prepared to deal with an urgent situation like the current health crisis. Finally, we explore 50 errors made by the best performing models on LitCovid documents and find that they often (1) correlate certain labels too closely together and (2) fail to focus on discriminative sections of the articles; both of which are important issues to address in future work. Both data and code are available on GitHub.